Scoring of an spectrum at the peak apex of an chromatographic elution peak. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>

Inheritance diagram for DIAScoring:

Public Member Functions
Constructors and Destructor

	DIAScoring ()
	Default constructor.
virtual	~DIAScoring ()
	Destructor.
Accessors

void	set_dia_parameters (double dia_extract_window, double dia_centroided, double dia_byseries_intensity_min, double dia_byseries_ppm_diff, double dia_nr_isotopes, double dia_nr_charges)
	set parameters for the algorithm
DIA Scores

void	dia_isotope_scores (const std::vector< TransitionType > &transitions, SpectrumType spectrum, OpenSwath::IMRMFeature *mrmfeature, double &isotope_corr, double &isotope_overlap)
	Isotope scores, see class description.
void	dia_massdiff_score (const std::vector< TransitionType > &transitions, SpectrumType spectrum, const std::vector< double > &normalized_library_intensity, double &ppm_score, double &ppm_score_weighted)
	Massdiff scores, see class description.
void	dia_by_ion_score (SpectrumType spectrum, AASequence &sequence, int charge, double &bseries_score, double &yseries_score)
	b/y ion scores
void	score_with_isotopes (SpectrumType spectrum, const std::vector< TransitionType > &transitions, double &dotprod, double &manhattan)
	Dotproduct / Manhatten score with theoretical spectrum.
Private Types


typedef OpenSwath::SpectrumPtr	SpectrumType
	Type definitions.
typedef OpenSwath::LightTransition	TransitionType
	Transition interface (Transition, Peptide, Protein).
typedef OpenSwath::LightPeptide	PeptideType
typedef OpenSwath::LightProtein	ProteinType
Private Member Functions
	DIAScoring (const DIAScoring &rhs)
	Copy constructor (algorithm class).
DIAScoring &	operator= (const DIAScoring &rhs)
	Assignment operator (algorithm class).
void	updateMembers_ ()
	Synchronize members with param class.
void	diaIsotopeScoresSub_ (const std::vector< TransitionType > &transitions, SpectrumType spectrum, std::map< std::string, double > &intensities, double &isotope_corr, double &isotope_overlap)
	Subfunction of dia_isotop_scores.
void	getFirstIsotopeRelativeIntensities_ (const std::vector< TransitionType > &transitions, OpenSwath::IMRMFeature *mrmfeature, std::map< std::string, double > &intensities)
DoubleReal	largePeaksBeforeFirstIsotope_ (double product_mz, SpectrumType &spectrum, double max_ppm_diff, double main_peak)
	Search for a large peak _before_ (lower m/z) the current peak.
DoubleReal	scoreIsotopePattern_ (double product_mz, const std::vector< double > &isotopes_int, int putative_fragment_charge)
	Compare an experimental isotope pattern to a theoretical one.
Private Attributes
double	dia_extract_window_
double	dia_centroided_
double	dia_byseries_intensity_min_
double	dia_byseries_ppm_diff_
double	dia_nr_isotopes_
double	dia_nr_charges_

Detailed Description

Scoring of an spectrum at the peak apex of an chromatographic elution peak.

In DIA (data independent acquisition) / SWATH analysis, at each chromatographic point a full MS2 spectrum is recorded. This class allows to compute a number of scores based on the full MS2 spectrum available. The scores are the following:

isotope scores: -- isotope_corr: computes the correlation of each fragment ion with the theoretical isotope distribution. -- isotope_overlap: checks whether a signal at position (mz - 1) / charge exists and how strong it is. This would be an indication that the current peak is an isotopic signal of another peak.

massdiff score: computes the difference in ppm of the experimental signal to the exepcted signal

b/y ion score: checks for the presence of b/y ions of the peptide in question

theoretical spectrum: a dotproduct and a manhattan score with a theoretical spectrum

This class expects spectra objects that implement the OpenSWATH Spectrum interface. Transitions are expected to be in the light transition format (defined in OPENSWATHALGO/DATAACCESS/TransitionExperiment.h).

Member Typedef Documentation

typedef OpenSwath::LightPeptide PeptideType [private]

typedef OpenSwath::LightProtein ProteinType [private]

typedef OpenSwath::SpectrumPtr SpectrumType [private]

Type definitions.

Spectrum type, see Spectrum interface

typedef OpenSwath::LightTransition TransitionType [private]

Transition interface (Transition, Peptide, Protein).

Constructor & Destructor Documentation

DIAScoring ( )

Default constructor.

virtual ~DIAScoring ( ) [inline, virtual]

Destructor.

DIAScoring ( const DIAScoring & rhs ) [private]

Copy constructor (algorithm class).

Member Function Documentation

void dia_by_ion_score	(	SpectrumType	spectrum,
		AASequence &	sequence,
		int	charge,
		double &	bseries_score,
		double &	yseries_score
	)

b/y ion scores

void dia_isotope_scores	(	const std::vector< TransitionType > &	transitions,
		SpectrumType	spectrum,
		OpenSwath::IMRMFeature *	mrmfeature,
		double &	isotope_corr,
		double &	isotope_overlap
	)

Isotope scores, see class description.

void dia_massdiff_score	(	const std::vector< TransitionType > &	transitions,
		SpectrumType	spectrum,
		const std::vector< double > &	normalized_library_intensity,
		double &	ppm_score,
		double &	ppm_score_weighted
	)

Massdiff scores, see class description.

void diaIsotopeScoresSub_	(	const std::vector< TransitionType > &	transitions,
		SpectrumType	spectrum,
		std::map< std::string, double > &	intensities,
		double &	isotope_corr,
		double &	isotope_overlap
	)			`[private]`

Subfunction of dia_isotop_scores.

void getFirstIsotopeRelativeIntensities_	(	const std::vector< TransitionType > &	transitions,
		OpenSwath::IMRMFeature *	mrmfeature,
		std::map< std::string, double > &	intensities
	)			`[private]`

retrieves intensities from MRMFeature computes a vector of relative intensities for each feature (output to intensities)

DoubleReal largePeaksBeforeFirstIsotope_	(	double	product_mz,
		SpectrumType &	spectrum,
		double	max_ppm_diff,
		double	main_peak
	)			`[private]`

Search for a large peak _before_ (lower m/z) the current peak.

This function will try to determine whether the current peak is part of an isotopic pattern that does NOT have the current peak as monoisotopic peak.

DIAScoring& operator= ( const DIAScoring & rhs ) [private]

Assignment operator (algorithm class).

void score_with_isotopes	(	SpectrumType	spectrum,
		const std::vector< TransitionType > &	transitions,
		double &	dotprod,
		double &	manhattan
	)

Dotproduct / Manhatten score with theoretical spectrum.

DoubleReal scoreIsotopePattern_	(	double	product_mz,
		const std::vector< double > &	isotopes_int,
		int	putative_fragment_charge
	)			`[private]`

Compare an experimental isotope pattern to a theoretical one.

This function will take an array of isotope intensities and compare them to the theoritcally expected ones using pearson correlation.

void set_dia_parameters	(	double	dia_extract_window,
		double	dia_centroided,
		double	dia_byseries_intensity_min,
		double	dia_byseries_ppm_diff,
		double	dia_nr_isotopes,
		double	dia_nr_charges
	)